3ZNX

Crystal structure of the OTU domain of OTULIN D336A mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZNVPDB ENTRY 3ZNV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5100 MM MES/IMIDAZOLE PH 6.5, 30 MM MGCL2, 30 MM CACL2, 10% PEG 4,000, 20% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.4549.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.807α = 90
b = 72.197β = 90
c = 94.843γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC QUANTUM 315rMIRROR2012-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3547.421000.099.96.1669083
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.371000.72.44.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ZNV1.3547.4763440338299.940.123490.121630.15894RANDOM18.363
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.37-0.40.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_dihedral_angle_4_deg21.292
r_sphericity_bonded20.514
r_dihedral_angle_3_deg12.849
r_rigid_bond_restr10.739
r_scangle_it6.607
r_scbond_it5.721
r_dihedral_angle_1_deg5.628
r_mcangle_it3.734
r_mcbond_it3.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_dihedral_angle_4_deg21.292
r_sphericity_bonded20.514
r_dihedral_angle_3_deg12.849
r_rigid_bond_restr10.739
r_scangle_it6.607
r_scbond_it5.721
r_dihedral_angle_1_deg5.628
r_mcangle_it3.734
r_mcbond_it3.222
r_mcbond_other3.206
r_angle_refined_deg1.462
r_angle_other_deg1
r_symmetry_vdw_refined0.354
r_xyhbond_nbd_other0.353
r_nbd_refined0.347
r_xyhbond_nbd_refined0.311
r_symmetry_vdw_other0.228
r_nbd_other0.222
r_nbtor_refined0.19
r_chiral_restr0.102
r_metal_ion_refined0.097
r_nbtor_other0.085
r_symmetry_hbond_refined0.059
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2094
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling